# asyncmd asyncmd is a library to write **concurrent** code to run and analyze molecular dynamics simulations using pythons **async/await** syntax. Computationally costly operations can be performed locally or submitted to a queuing system. asyncmd enables users to construct complex molecular dynamics (MD) workflows or develop and implement trajectory based enhanced sampling methods with the following key features: - flexible, programmatic and parallel setup, control, and analysis of an arbitrary number of MD simulations - dictionary-like interface to the MD parameters - parallelized application of user defined (python) functions on trajectories (including the automatic caching of calculated values) - propagation of MD until any or all user-supplied conditions are fulfilled on the trajectory - extract molecular configurations from trajectories to (re)start an arbitrary number of MD simulations from it **If you use asyncmd in published research please consider citing it as:** - Hendrik Jung and Gerhard Hummer, (2025). asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems. Journal of Open Source Software, 10(112), 8321, ## Get started This section contains everything to get you started using asyncmd. ```{toctree} :maxdepth: 2 :caption: The Basics usage/installation usage/basic_gromacs_example ``` You might also want to have a look at the [example jupyter notebooks](example-notebooks) below. ## User guide This section provides more in-depth explanations on various topics, such as the {py:class}`Trajectory ` object or the use of complex stopping criteria for MD simulations. It also includes a section on modifying and extending asyncmd for your own use-case. ```{toctree} :maxdepth: 2 :caption: User guide guide/trajectories_trajectoryfuncs_and_caching guide/frame_extraction_and_trajectory_concatenation guide/trajectory_propagation guide/gromacs guide/configuration guide/utils guide/extending_asyncmd ``` ## Community guide The following section contains information on how to get help and/or report any issues encountered using asyncmd as well as how to contribute code or documentation. ```{toctree} :maxdepth: 2 :caption: Community community/support community/contributing ``` (example-notebooks)= ## Example notebooks This section contains example jupyter notebooks (also included in the repository) on various topics and starts with a brief description of all notebooks. ```{toctree} :maxdepth: 2 :caption: Example notebooks :titlesonly: Overview ``` ---------------- ```{toctree} :maxdepth: 1 :caption: Module layout module_layout_autosummary ``` ```{toctree} :maxdepth: 2 :caption: Changelog and Indices include_changelog modindex genindex ```